
$geno ="geno.bgl";
$marker ="markers.txt";
$reference ="phased.bgl";

#$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_quatermb";
#$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_halfmb_seed1";  
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_halfquatermb";  
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_quaterquatermb";  
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_halfmb";      
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_halfmb_seed2";  
$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_4mb1mbedge";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_4mb1mbedge";
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 4000000 -e 1000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
=head
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1000genome/genome1000_halfmb_seed2";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 2000000 -e 500000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);

=head
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/genome1000_quatermb";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 2000000 -e 250000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/genome1000_halfquatermb";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 2000000 -e 125000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);

$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/genome1000_quaterquatermb";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 2000000 -e 62500 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);


$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/quaterquatermb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/halfquatermb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/quatermb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/halfmb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1mb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/2mb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/4mb_1000samples";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
=temp
$geno ="geno.bgl";
$marker ="markers.txt";
$reference ="phased.bgl";

$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/quaterquatermb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 62500 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);

$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/halfquatermb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 125000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);

$tempdir ="/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/quatermb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 250000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);

$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/halfmb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 500000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);


$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/1mb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 1000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);


$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/2mb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 2000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);

$tempdir = "/data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/chr22/4mb_1000samples";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 4000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system($sys);
#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quaterquatermb_seed";
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");

#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfquatermb";
=head
$geno ="geno.bgl";
$marker ="markers.txt";
$reference ="phased.bgl";
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/4mb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/4mb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 4000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/2mb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/2mb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 2000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/1mb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/1mb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 1000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfmb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfmb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 500000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quatermb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quatermb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 250000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfquatermb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfquatermb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");

#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 125000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quaterquatermb_seed1";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quaterquatermb_seed";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 62500 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfquatermb";
#$tempdir ="/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quaterquatermb";
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 62500 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 125000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/quatermb";
#$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 250000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
#system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
=head
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/1mb";
$geno ="geno.bgl";
$marker ="markers.txt";
$reference ="phased.bgl";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 1000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
#system($sys);
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/2mb";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl  -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 2000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/4mb";
$sys = "/usr/bin/perl  /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 4000000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
$tempdir = "/data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/clean/beagle/run_beagle/chr22/halfmb";
$sys = "/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_chop_beagle_files_new_research.pl -s $tempdir/$geno -m $tempdir/$marker -r $tempdir/$reference -w 10000000 -e 500000 -d $tempdir > $tempdir/perl_chop_beagle_files.log";
#system($sys);
system("/usr/bin/perl /data1/bsi/BORA_processing/devel/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/bin/perl_after_imputation_merge_research.pl -d $tempdir");
=cut
